Login or Register to Ask a Question and Join Our Community


Shell Programming and Scripting

AWK command

Login to Discuss or Reply to this Discussion in Our Community

 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting AWK command
# 1  
Old 03-12-2012
AWK command
Code:
dr=`awk 'BEGIN{s=0}{s = s + $7^2 + $8^2 + $9^2}END{print sqrt(s)}' diff.pdb

`


I have a matrix with columns $7, $8, $9 of interest. What exactly is this AWK routine doing. Is this a loop, and if so, where are the bounds of the loop? Is it looping over each record? This is not my script, am just trying to understand what it does.
# 2  
Old 03-12-2012
Code:
dr=`awk 'BEGIN{s=0}{s = s + $7^2 + $8^2 + $9^2}END{print sqrt(s)}' diff.pdb`

The red part executes once for every line in the file; BEGIN {} at the beginning when no lines have been read, END {} after all lines have been read.
# 3  
Old 03-12-2012
It is taking each of the values found in columns 7, 8 and 9 to the second power, then aggregating those square values in variable "s". After doing that for all the records in the file is printing the square root of the variable "s".
# 4  
Old 03-12-2012
Consider values in test.pdb
Code:
ATOM      1  CAY ALA X   2      14.962  52.147  1.00  1.00       DIAL

Now, on my calculator
Quote:
sqrt(14.962^2 + 52.147^2 + (-10.171)^2)
gives 55.196


awk '{print sqrt($7^2 + $8^2 + $9^2)}' test.pdb
gives 54,7723



Could someone please try to explain this?




Consider a more difficult case called test2.pdb
Code:
ATOM      1  CAY ALA X   2      14.962  52.147 -10.171  1.00   1.00      DIAL
ATOM      5  CY  ALA X   2      14.566  51.759 -11.567  1.00  1.00       DIAL

Code:
awk 'BEGIN{s=0}{s = s + $7^2 + $8^2 + $9^2}END{print sqrt(s)}'  test2.pdb

gives

76,9285
# 5  
Old 03-12-2012
The value of $9 is missing in test.pdb. If I put in -10.171, I get 55.1925 and I get 55.1925 and also on my calculator. Maybe you made a typo?
test2.db gives 77.9203 with awk and also on the calculator...
This User Gave Thanks to Scrutinizer For This Post:
chrisjorg
# 6  
Old 03-12-2012
Could you show me exactly what computation you do?

---------- Post updated at 04:47 PM ---------- Previous update was at 04:30 PM ----------

Ok, thanks. I got it now....
Login or Register to Ask a Question

Previous Thread | Next Thread

8 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Pass awk field to a command line executed within awk

Hi, I am trying to pass awk field to a command line executed within awk (need to convert a timestamp into formatted date). All my attempts failed this far. Here's an example. It works fine with timestamp hard-codded into the command echo "1381653229 something" |awk 'BEGIN{cmd="date -d... (4 Replies)
Discussion started by: tuxer
4 Replies

2. Shell Programming and Scripting

Multiple command execution inside awk command during xml parsing

below is the output xml string from some other command and i will be parsing it using awk cat /tmp/alerts.xml <Alert id="10102" name="APP-DS-ds_ha-140018-componentFailure-S" alertDefinitionId="13982" resourceId="11427" ctime="1359453507621" fixed="false" reason="If Event/Log Level(ANY) and... (2 Replies)
Discussion started by: vivek d r
2 Replies

3. Shell Programming and Scripting

awk command to compare a file with set of files in a directory using 'awk'

Hi, I have a situation to compare one file, say file1.txt with a set of files in directory.The directory contains more than 100 files. To be more precise, the requirement is to compare the first field of file1.txt with the first field in all the files in the directory.The files in the... (10 Replies)
Discussion started by: anandek
10 Replies

4. Shell Programming and Scripting

awk command in script gives error while same awk command at prompt runs fine: Why?

Hello all, Here is what my bash script does: sums number columns, saves the tot in new column, outputs if tot >= threshold val: > cat getnon0file.sh #!/bin/bash this="getnon0file.sh" USAGE=$this" InFile="xyz.38" Min="0.05" # awk '{sum=0; for(n=2; n<=NF; n++){sum+=$n};... (4 Replies)
Discussion started by: catalys
4 Replies

5. Shell Programming and Scripting

awk command for simple join command but based on 2 columns

input1 a_a a/a 10 100 a1 a_a 20 200 b1 b_b 30 300 input2 a_a a/a xxx yyy a1 a1 lll ppp b1 b_b kkk ooo output a_a a/a 10 100 xxx yyy (2 Replies)
Discussion started by: ruby_sgp
2 Replies

6. UNIX for Dummies Questions & Answers

Basic awk question...getting awk to act on $1 of the command itself

I have a script problem that I am not able to solve due my very limited understanding of unix/awk. This is the contents of test.sh awk '{print $1}' From the prompt if I enter: ./test.sh Hello World I would expect to see "Hello" but all I get is a blank line. Only then if I enter "Hello... (2 Replies)
Discussion started by: JasonHamm
2 Replies

7. Shell Programming and Scripting

awk/sed Command : Parse parameter file / send the lines to the ksh export command

Sorry for the duplicate thread this one is similar to the one in https://www.unix.com/shell-programming-scripting/88132-awk-sed-script-read-values-parameter-files.html#post302255121 Since there were no responses on the parent thread since it got resolved partially i thought to open the new... (4 Replies)
Discussion started by: rajan_san
4 Replies

8. Shell Programming and Scripting

assign a command line argument and a unix command to awk variables

Hi , I have a piece of code ...wherein I need to assign the following ... 1) A command line argument to a variable e.g origCount=ARGV 2) A unix command to a variable e.g result=`wc -l testFile.txt` in my awk shell script When I do this : print "origCount" origCount --> I get the... (0 Replies)
Discussion started by: sweta_doshi
0 Replies
Login or Register to Ask a Question